A total of 272 strains of filamentous fungi were isolated from soil, leaves of coffee plants and coffee cherries collected in coffee-growing areas of Mexico on three semi-synthetic culture media containing coffee extract, coffee extract with sucrose and coffee pulp extract. The isolated strains were purified by conventional techniques and identified by microscopic examination. Strains were selected on the basis of their caffeine-degrading ability in well-defined liquid medium containing caffeine. Most of the isolated microorganisms belong to Aspergillus, Penicillium, Trichoderma, Fusarium, and Humicola genera. Five strains belonging to Aspergillus species and two strains belonging to Penicillium species had the ability to degrade almost 100% of the caffeine in liquid medium. A comparative study on the evaluation of natural microflora present in coffee pulp and coffee husk revealed the presence of a wide variety of microorganisms. The percentage distribution of fungi, bacteria and yeast was almost similar in all the samples, except in coffee husk where the fungal population was slightly higher than in the other two samples. The yeast population was predominant when the coffee pulp was lyophilized immediately after pulping. However, there was a wide diversity in the microbial population with respect to selective media containing functional nutritional groups like cellulose, starch and pectin.